The Pope made a speech to the Queen of England
which could be interpreted as comparing atheists to Nazis
As we reflect on the sobering lessons of atheist extremism of the 20th century, let us never forget how the exclusion of God, religion and virtue from public life leads ultimately to a truncated vision of man and of society and thus a reductive vision of a person and his destiny.
I leave open the question of whether Pope Benedict XVI prefers the sobering lessons of religious extremism from the 16th and 17th Centuries. It's true that many of the violent extremists of the 20th Century were explicitly atheistic: Stalin and other Soviets, the Chinese Cultural Revolution, and the Khmer Rouge. But many other violent extremists were religious, even if their target selection wasn't motivated by religion. U.S. segregationists and South African apartheid advocates, conflicts in Rwanda, Guatemala, Vietnam... World Wars I and II were not about religion, but aside from the Soviets, all the major players were at least nominally religious. And regardless of the private views of Nazi leaders, their extremist persecutions were largely ethnic and social, not religious: being a nonpracticing Jew didn't buy reprieve, nor did they distinguish between Christian and atheist homosexuals.
Leonard Shlain wrote something interesting in The Alphabet vs. The Goddess
: the conflicts between communism/socialism and capitalism in 19th and 20th Century Europe can be seen as a new phase in the continent's history of religious warfare. The communists don't believe in God, but they have religious texts (Das Kapital, for instance), prophets, and a sometimes-violent fervor based on a set of ideas.
So far the 21st Century has provided one major ideological conflict: Wahhabists
and other extremist Islamic groups in a decentralized fight against imperialism and secular and insufficiently-religious governments. And there are conflicts which mix nationalism with religion that have spilled over from the last century: Israelis and Palestinians in the near east and Muslims and Hindus in Pakistani/Indian border lands. But the bloodiest conflicts, in eastern Congo and southern Sudan, are about concerns much older than religious conflict: land and resources. And as the world population grows and the climate gets more volatile, these sorts of conflicts can only be expected to spring up more often. The important thing isn't what the folks involved believe, it's what they have and what they want.